if there is little sequence similarity between host and parasite (which I assume is the case) you can use a default RNA-seq pipeline to analyse it as Bjoern mentioned. I would do two separete analyses then: with the host ref genome and with the parasite ref genome.

If you also do both for the host-only dataset, you will also get an idea of how many reads from your host would map to your parasite genome. If this "cross-mapping" would be problematic, you could make an artificial ref containing both the host and parasite (and e.g. only consider unique mapping as a start point)

Yes I tend to agree, my thought is how I should do it when for the set that
contains the host/pathogen transcripts. Do I align to the host first and
then align anything else that isn't aligned to the pathogen genome? Is this
a reasonable thing to do?